Biology subjects

Li, W.

Publications and source records attributed to Li, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

The cleaved C-terminal domain of GmERS1-1 modulates cell cycle via GmACR1

Ethylene signaling orchestrates plant development and stress adaptation, yet how post-translational modifications of its receptors coordinate growth regulation remains unresolved. Here, we uncover a proteolytic processing mechanism of the soybean ethylene receptor GmERS1-1 that directly gates cell cycle progression. The GmERS1-1 mutants exhibit elevated yield under field conditions, whereas overexpression suppresses growth and hypersensitizes plants to ethylene. Ethylene triggers nuclear translocation of C-terminal domain (GmERS1-1-CEND), which is indispensable for receptor function. Mechanistically, GmERS1-1-CEND scaffolds a trimeric complex with GmACR1 and GmCDK7, enforcing G2/M phase arrest, thereby decoupling cell division from canonical ethylene transcriptional responses. Strikingly, ethylene-induced cell cycle blockade during apple fruit maturation mirrors this pathway, suggesting deep conservation across angiosperms. Our work defines a receptor processing-dependent signaling axis that directly interlinks phytohormone perception with cell cycle control, proposing tunable targets (e.g., GmERS1-1 cleavage efficiency) for engineering crop architecture and productivity.

plant biology↗

bioRxiv2026

Long-form hibernation-promoting factor coordinates 100S assembly and translational repression

Ribosome hibernation mediated by long-form hibernation-promoting factor (HPF) requires coordination of ribosome dimerization and translational repression, but how these functions are integrated remains unclear. Here, we present cryo-EM structures of native 100S from a deep-sea Bacillus isolate, revealing a conformationally heterogeneous 100S population. Beyond the established roles of the HPF N-terminal domain (NTD) in decoding-center occlusion and the C-terminal domain (CTD) in dimerization, our analyses reveal additional contributions from the Linker and a charged CTD surface near the 16S rRNA 3' terminus containing the anti-Shine-Dalgarno (aSD) sequence. Linker substitutions differentially affect translational repression while retaining 100S formation, with distinct effects of the two Linker segments. Mutation of the charged CTD surface enhances translational repression while retaining robust 100S formation, suggesting an additional role beyond CTD-mediated ribosome dimerization. Functional analyses in an E. coli cell-free translation system further show that the inhibitory activity of individual HPF regions varies with translational context. Together, these findings support a modular model in which the NTD, Linker, and CTD make distinct but interconnected contributions to 100S assembly and translational repression.

biochemistry↗

bioRxiv2026

Transient tubular membrane injury is converted into persistent fibrosis through a macrophage-fibroblast relay

A central unresolved problem in acute kidney injury (AKI) is how a transient epithelial insult is converted into persistent fibrotic repair that drives progression toward chronic kidney disease. Although tubular, immune and stromal responses are individually well recognized, the mechanistically continuous relay linking these three compartments has remained unresolved. Here we define a directional information-conversion pathway spanning injured tubular epithelial cells, macrophages and fibroblasts. Time-resolved single-cell profiling identified a TREM2/SPP1 macrophage state that emerged as post-ischemic repair became fibrotic. Tubular injury remodeled phosphatidylserine (PS) species, increased oxidized PS and PS externalization, and generated a membrane-lipid context for TREM2 sensing, supported by PS masking, defined liposomes and orthogonal binding assays. Structure-function analysis separated R47-dependent phospholipid recognition from K183-dependent DAP12 coupling, linking membrane damage to SYK activation and NF-kB/AP-1-driven Spp1 transcription. Macrophage-derived SPP1 then activated ITGAV/ITGB1-associated FAK-SMAD2/3 signaling, fibroblast contraction and matrix production. Crucially, repair-phase SPP1 neutralization and post-injury Cx3cr1-lineage Trem2 deletion attenuated fibrosis, with delayed Trem2 deletion protective in both ischemic and obstructive injury. Human single-cell, spatial, urinary and tissue analyses showed cross-species and cross-scale convergence. These findings resolve how transient tubular membrane damage is successively transformed across three cellular compartments into persistent, yet interruptible, fibrotic repair.

pathology↗

bioRxiv2026

Chronic Social Isolation Reshapes the Metabolome in Drosophila

Sleep, feeding, and metabolism are tightly coordinated outputs of the circadian system. Previous studies showed that chronic social isolation reduces sleep and increases feeding in Drosophila. Here, untargeted metabolomic profiling revealed that chronic social isolation induces a distinct metabolomic signature spanning amino acids, carbohydrates, and lipids, establishing a foundation for understanding the physiological consequences of social isolation.

neuroscience↗

bioRxiv2026

Environmental modulation of social isolation-induced sleep loss in Drosophila

Chronic social isolation induces persistent behavioral and physiological changes across species. In humans, prolonged social isolation is associated with insomnia and increased risks of cognitive decline, cardiovascular disease, compromised immunity, and premature mortality. Yet whether these consequences are modified by the environment in which social isolation is experienced remains unclear. In particular, can access to social sensory information from conspecifics alleviate the effects of isolation and can various ambient environmental settings modify them? A related question arises during behavioral measurement because behavioral assays themselves impose a new environmental context. Whether these assays simply capture the enduring effects of prior social experience or further modify those effects remains unknown. Using social isolation-induced sleep loss in Drosophila as a model, we systematically examined how the social, spatial, and photoperiodic environments during isolation and behavioral monitoring influence the isolation phenotype. Providing isolated flies with visual, olfactory, or tactile social cues from conspecifics living behind a divider, either individually or in combination, was insufficient to alleviate sleep loss. Spatial confinement exacerbated isolation-induced sleep loss, while winter-like photoperiod in spatially confined Drosophila Activity Monitor assays revealed the clearest progressive decline in sleep during sleep monitoring. Together, these findings demonstrate that social isolation-induced sleep loss is both enduring and dynamic: it persists despite exposure to social cues yet remains sensitive to the environmental context in which isolation is experienced and behavior is measured. More broadly, our study establishes a tractable framework for investigating the environmental modulation of chronic social isolation.

neuroscience↗

bioRxiv2026

Direct optogenetic activation of inner hair cells improves the efficiency and fidelity of auditory encoding

Severe hearing impairment affects approximately 5% of the global population, with a prevalence projected to increase over the coming decades. Cochlear implant devices pose a neuroprosthetic treatment option to allow sound perception and speech comprehension. However, users are limited in the spectrum of auditory information they can regain because electrical stimulation of the auditory nerve generates a broad spread of current and limits the transmission of sound frequency information. Recently, optogenetic stimulation of the cochlear nerve has emerged as a promising alternative for hearing restoration. Because light can be precisely confined in space, optogenetic stimulation of the cochlea permits to activate auditory neurons within smaller tonotopic regions, thereby improving the encoding of sound frequencies compared to electrical stimulation. However, this approach is limited in terms of dynamic range and ability to follow rapidly varying inputs, thus preventing faithful transmission of auditory information. Here, we developed an alternative approach targeting directly sensory inner hair cells with optogenetics. We demonstrate that this approach decreases the amount of light energy necessary to evoke auditory responses. Direct stimulation of hair cells increases the dynamic range of intensities encoded by neurons in subcortical auditory areas and improves the temporal fidelity of optogenetic responses. Finally, a biophysical model of the auditory system suggests that preserving the synapses between inner hair cells and auditory neurons greatly improves the encoding performance of an optical cochlear implant. Together, our results suggest that targeting sensory inner hair cells is a promising approach for hearing restoration through an optical implant.

neuroscience↗

bioRxiv2026

Early life social isolation primes flies for more rapid TDP-43 dependent neurodegeneration later in life.

A key pathophysiological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is loss of nuclear localization and abnormal cytoplasmic aggregation of TAR DNA-binding protein 43 (TDP-43). Upstream factors that trigger the onset and progression of such neurodegenerative diseases are largely unknown. Aging and environmental factors contribute as potential risk factors. But epidemiological evidence suggests psychological stressors such as social isolation and loneliness are also associated with increased risks of neurodegenerative disease [1-8]. We examined the impacts of social isolation on TDP-43 related neurodegeneration. To investigate the potential for causative impact on neurodegeneration, we compared the effects of social isolation versus social enrichment in Drosophila. We utilized an established social isolation paradigm in which flies were either housed alone or in groups as young adults. We found that early-life social isolation acts as a primer to exacerbate the rate of neurodegeneration in response to subsequent induction of pathological levels of TDP-43. Social isolation stress drives more rapid activation of mdg4, an endogenous retrovirus that functionally mediates TDP-43 effects and more aggressive propagation of TDP-43 protein pathology from surface glial cells to nearby neurons. Shortened life span also ensues. We demonstrate that providing isolated flies with visual, olfactory and tactile social cues from conspecifics living behind a divider was insufficient to alleviate these effects of social isolation on neurodegeneration. Our findings have implications for the association between psychological stressors such as loneliness and risk of neurodegenerative diseases in humans and provide a platform to investigate mechanistic underpinnings in animal models.

neuroscience↗

bioRxiv2026

Agentic transcranial functional ultrasound imaging: @fUS

Functional ultrasound (fUS) imaging provides deep, wide-field access to brain function, but instrument cost and complex acquisition and analysis workflows restrict its wider adoption. Here we introduce @fUS, an agentic transcranial imaging platform with an open architecture that integrates purpose-built hardware with executable experimental skills and persistent structured memory. The system combines 128-channel, 16-bit acquisition at 125 MHz with GPU-based processing and enables functional imaging through the intact scalp and skull of mice, with approximately 100-m spatial resolution and 10-Hz temporal sampling, providing a basis for longitudinal studies without cranial-window surgery. Its agent connects scientific objectives to experimental design, direct instrument control and data analysis, retaining context across interactions and supporting inspectable workflows through text and hands-free voice control. Neuroscience trainees with limited engineering experience independently configured the system within 30 min. Agent-assisted exploration of whisker-stimulation datasets revealed low-frequency vascular changes beyond conventional response mapping, supported by complementary two-photon measurements of single-vessel diameter. By combining transcranial imaging with accessible instrument control and analysis, @fUS provides a foundation for wider adoption and larger, more diverse neuroscience datasets. More broadly, it offers a framework for scientific instruments in which measurement, computation and experimental reasoning are developed as parts of the same system.

bioengineering↗

bioRxiv2026

Systemic tumor-cell reprogramming converts solid tumors into in situ biofactories for immunotherapy

A central challenge in oncology is delivering potent drugs to tumors without harming healthy tissues. We therefore asked whether tumor cells themselves could be genetically programmed to produce therapeutic molecules directly within the tumor. We present LENTRA (LENtiviral Tumor-Reprogramming Activator), an antigen-targeted lentiviral platform that enables selective transduction and genetic modification of tumor cells in vivo. Following intravenous administration, LENTRA achieves tumor restricted expression of immune checkpoint inhibitors, cytokines, or therapeutic enzymes in multiple murine solid tumor models. Local production of anti CTLA 4 or IL 12 triggered potent antitumor responses while avoiding systemic toxicities. Tumor restricted secretion of sialidase enhanced dendritic cell and T cell infiltration, and reprogrammed tumor associated macrophages toward an immunostimulatory phenotype, resulting in tumor regression and durable immune memory, including in tumors with heterogeneous antigen expression. In patient derived tumor explants, LENTRA mediated efficient transduction, immune remodeling, and reduced tumor viability. By engineering tumors to produce therapeutic proteins, LENTRA converts resistant tumors into autonomous therapeutic sources and active immune hubs, achieving local TME reprogramming and systemic antitumor immunity with an improved safety profile.

cancer biology↗

bioRxiv2026

aaRSID, an engineered pyrrolysyl-tRNA synthetase platform for multi-probe proximity proteomics

Proximity labeling (PL) methods utilize spatially targeted chemical or enzymatic generation of a diffusible, reactive intermediate to covalently tag neighboring proteins in living systems. Unlike other tools for studying molecular interactions, PL can detect transient protein relationships with high spatial and temporal sensitivity, allowing for insight into their roles in biological processes. However, current enzymatic PL tools, such as TurboID and APEX2, are limited by their substrate structure and chemistry, which can generate significant background and/or perturb cellular physiology. To address these limitations, we have developed aminoacyl-tRNA synthetase ID (aaRSID), a PL tool that leverages an engineered pyrrolysyl tRNA synthetase (PylRS) for proximity labeling of proteins. We chose PylRS because it can catalyze promiscuous lysine labeling in the absence of its cognate tRNA and utilize a variety of non-canonical amino acids (ncAAs) as substrates. Here, we demonstrate aaRSID's intrinsic proximity labeling activity, use directed evolution to improve this activity, and apply the improved mutant (aaRSID-Ma1.3) for subcellular proteomics and multiplexed imaging. Our work establishes aminoacyl-tRNA synthetases as a new PL enzyme class and introduces a versatile chemical platform for developing ncAA-derived probes to map cellular microenvironments, greatly expanding the applications possible of PL technology.

biochemistry↗

bioRxiv2026

A germline-specific reporter reveals conserved primordial germ cell developmental dynamics between jawless and jawed fish species

Primordial germ cells (PGCs) are the stem cell lineage responsible for transmitting genetic information across generations and are therefore central to studies of germline development, reproduction, and evolution. However, a lack of molecular tools in jawless vertebrates such as lampreys and hagfish has limited comparative insights into the evolutionary origins of vertebrate germline cells. Here, we report the development of the first germline-specific reporter (GSR) in the sea lamprey (Petromyzon marinus), Tg(piwil1: egfp-UTRnanos1), a piwil1-based germline reporter that is driven by the sea lamprey piwil1 regulatory region that directs Green Fluorescent Protein (GFP) expression in early PGCs. Promoter activity was validated by robust GFP expression in PGCs of zebrafish embryos co-injected with Tol2 transposase mRNA. Injection of the construct into sea lamprey embryos resulted in early, persistent, and gonad-localized GFP-positive cells. These results demonstrate stable germline-specific transgene expression in a jawless vertebrate and suggest deep evolutionary conservation of germline regulatory mechanisms between jawless and jawed vertebrates. Furthermore, the piwil1-based germline reporter line enabled lifetime visualization of zebrafish germline cells, revealing that increased PGC abundance during embryogenesis biases toward female sexual differentiation. Together, this study establishes the first GSR system in a jawless vertebrate and provides a useful platform for investigating germline biology and vertebrate germline evolution.

developmental biology↗

bioRxiv2026

The RNA modification N6-methyladenosine restrains SIRPα to license myeloid efferocytosis in atherosclerosis

Background: Macrophages participate in atherosclerotic plaque development, progression and resolution, integrating lipid and inflammatory cues to balance tissue damage and repair. Despite considerable understanding of macrophage function in atherosclerosis, the underlying regulatory mechanisms governing these responses continue to evolve. Emerging evidence implicates epitranscriptomic gene regulation by the RNA modification N6-methyladenosine (m6A) in control of context specific immune responses, but its role in atherosclerosis is not well-defined. Methods: We integrated m6A quantitative trait loci (m6A QTLs) with Coronary Artery Disease (CAD) GWAS summary statistics. Using Oxford Nanopore direct RNA sequencing and MeRIP-seq, we constructed a high-resolution map of m6A modifications in macrophages. To determine the functional consequences of myeloid m6A loss in-vivo, we generated a myeloid-specific loss-of-function mouse model of m6A (Mettl14f/f LysMCre) and performed atherosclerosis studies using bone marrow transplantation into irradiated Ldlr-/- mice. Atherosclerosis lesions were analyzed using light microscopy and immunofluorescence imaging, with complementary in-vitro mechanistic studies performed in murine bone marrow derived macrophages (BMDMs). Results: m6A quantitative trait loci (m6A-QTLs) were enriched in CAD GWAS loci relevant to immune and lipid function, implicating m6A regulation in human CAD genetics. Using Oxford Nanopore direct RNA sequencing in conjunction with public MeRIP-sequencing data, we generated a single-base resolution, stoichiometric map of m6A modification in macrophages, nominating genes central to macrophage biology in atherosclerosis as high-confidence m6A targets. Myeloid specific deletion of the m6A "writer" complex subunit Mettl14 drove the development of larger, more necrotic and unstable atherosclerotic plaques on an Ldlr-/- background compared with Mettl14f/f controls, establishing an atheroprotective role for myeloid m6A. Loss of myeloid Mettl14 impaired macrophage efferocytosis in atherosclerotic plaques, in a dexamethasone-induced apoptosis in the thymus and in-vitro. Molecularly, m6A methylation of the "don't eat me" antiphagocytic receptor SIRP RNA suppressed its protein expression. Conclusions: These findings identify the myeloid m6A - SIRP axis as a novel homeostatic regulator of efferocytosis and establish epitranscriptomic remodeling as a crucial layer of macrophage regulation in atherosclerosis.

physiology↗

bioRxiv2026

Latent generative search unlocks de novo design of untapped biomolecular interactions at scale

De novo protein design has advanced rapidly, yet designing binders to polar, solvent-exposed epitopes and small, flexible ligands remains challenging. Such hydrated surfaces and flexible molecules, including carbohydrates, provide few of the hydrophobic contacts favoured by current methods and have largely resisted de novo binders. To address this challenge, here we introduce latent generative search for binder design, a novel framework that uses reward-guided search at inference time to steer the Proteina-Complexa generative model. The model codesigns sequence and structure - generating them together in a continuous latent space - and thereby removes the inverse-folding step on which current methods rely. In a screen of more than one million designs by multiplexed phage display, latent generative search produced more validated binders than every other method tested, its codesigned sequences surpassing post hoc redesign. It delivered high-affinity binders across therapeutic receptors, a viral attachment protein and intracellular signalling targets. Our approach also accessed previously untapped biology, generating the first de novo proteins that bind a free carbohydrate, including one that discriminates between blood-group antigens - a polar, flexible target class beyond the reach of current design methods.

bioengineering↗

bioRxiv2026

Spatially Confined Phase Separation Promotes Local Tubulin Availability to Stabilize Ciliary Microtubule Growth

How microtubule (MT) growth is locally sustained within cilia remains a central unanswered question in ciliogenesis. Here we identify RAT-1 as a regulator of ciliary tubulin homeostasis and MT growth. Genetic screens in Caenorhabditis elegans show that loss of RAT-1 suppresses the toxic effects of a mutant -tubulin and restores ciliary structure, while RAT-1 deficiency reduces tubulin turnover at the ciliary tip, indicating its physiological role in tuning ciliary MT dynamics. Mechanistically, RAT-1 forms intra-ciliary condensates selectively at the distal region through an auto-inhibitory -helix and phosphorylation by the distally localized ciliary kinase. RAT-1 enriches tubulin within condensates in vivo/vitro, and cooperates with end-binding proteins to facilitate sustained MT growth in vitro. Notably, heterologous expression of worm RAT-1 reveals conserved condensate behavior within mammalian cilia. Our findings reveal a kinase-regulated mechanism controlling RAT-1 condensation within cilia and establish RAT-1 as a regulator of ciliary MT dynamics.

cell biology↗

bioRxiv2026

LRRC37A is essential for acrosomal ion homeostasis and male fertility

Mammalian spermatozoa face various challenges during their long march to the destination. As a specialized membrane-bound organelle in the sperm head, the acrosome is particularly sensitive to changes in ionic and osmotic conditions, yet how acrosomal ion homeostasis is maintained remains largely unknown. Here, we show that LRRC37A is required for acrosomal ion homeostasis. Loss of Lrrc37a causes complete male infertility, accompanied by pronounced enlargement and deformation of the acrosome in the sperm head. Acrosome biogenesis was not affected by Lrrc37a knockout during the early stages of spermiogenesis, whereas acrosomal enlargement emerged at later stages and became more pronounced in the epididymis. LRRC37A localized to the outer acrosomal region and interacted with the Na/K-ATPase -subunit isoforms ATP1A1 and ATP1A4. Loss of LRRC37A disrupted the spatial distribution of both isoforms and was accompanied by increased Na within the acrosomal region. In addition, pharmacological perturbation of Na/K-ATPase activity or cellular ion homeostasis induced acrosomal swelling. These findings establish an essential role for LRRC37A in acrosomal ion homeostasis, suggesting that its deficiency may be associated with a distinct form of teratozoospermia characterized by acrosomal enlargement.

cell biology↗

bioRxiv2026

Integrating structural and biological evidence to rerank ESMFold2 protein-protein interactions

Large-scale protein structure prediction enables proteome-wide protein-protein interaction (PPI) screening, but distinguishing biologically meaningful interactions from spurious interfaces remains challenging. Here, we develop a scalable framework combining fast, MSA-free ESMFold2 prediction with PAE-guided domain parsing and evidence-based reranking. Three-recycle ESMFold2-Fast achieved 57% acceptable-or-better DockQ scores on FoldBench, comparable to AlphaFold2-Multimer while substantially reducing computation. PAE-guided parsing preserved 98.1% of XL-MS cross-links within parsed domain pairs. We then developed the Structure Prediction and Omics informed Classifier (SPOC)-ESMFold2, which integrates structural features with independent biological evidence to prioritize predicted interactions. SPOC-ESMFold2 achieved an AUROC of 0.93 and AUPR of 0.90, compared with 0.87 and 0.79 for a structural-only classifier. Under a 1:128 positive-to-negative ratio, SPOC-ESMFold2 achieved 17.2% recall at 5% false-discovery rate, substantially outperforming structural confidence metrics alone. This framework enables scalable PPI screening by integrating structural plausibility with orthogonal biological evidence to prioritize candidates for experimental investigation.

bioinformatics↗

bioRxiv2026

A Tumor-Pituitary-Stromal Axis Promotes Colorectal Cancer Progression

Peripheral tumors can reprogram systemic physiology, yet how they engage central endocrine organs to remodel the local tumor microenvironment is unknown. We found that colorectal cancer (CRC) elevates circulating BMP2, which activates pituitary signaling and enhances endocrine output. Increased pituitary-derived growth hormone acted on growth hormone receptor-expressing cancer-associated fibroblasts (CAFs), inducing a p21-dependent senescence-like state and tumor-promoting secretory program. Disruption of pituitary BMP signaling or fibroblast GHR reduced tumor growth, whereas fibroblast-specific depletion of p21 abrogated GHR-dependent tumor promotion. In patients with CRC, elevated pituitary metabolic activity correlated with stromal p21 expression and tumor burden. Our study reveals a tumor-pituitary-stromal signaling axis through which a peripheral malignancy recruits a central endocrine organ to remotely shape its own microenvironment and promote disease progression.

cancer biology↗

bioRxiv2026

TGF-β- and IL-1-dependent fibroblast states differentially shape pancreatic cancer microenvironments and metastasis

Pancreatic ductal adenocarcinoma (PDAC) contains heterogeneous cancer-associated fibroblast (CAF) populations, including interleukin 1 (IL-1)-dependent inflammatory CAFs (iCAFs) and transforming growth factor beta (TGF-{beta})-dependent myofibroblastic CAFs (myCAFs), whose functions at primary and metastatic sites remain incompletely defined. Here, we genetically disrupted IL-1 or TGF-{beta} signalling in fibroblast activation protein (FAP)-expressing CAFs arising from a shared cellular origin to determine how myCAF and iCAF states shape PDAC progression and microenvironments. Depletion of TGF-{beta}-dependent myCAFs, but not IL-1-dependent iCAFs, did not alter primary tumour growth or local metastatic dissemination but significantly reduced liver and lung metastases. Matched primary tumours and liver metastasis analyses also revealed site-specific stromal responses to TGF-{beta} signalling disruption. Experimental models of liver metastasis colonisation and outgrowth indicated that the reduced metastatic phenotype was linked primarily to alterations within pancreatic tumours rather than to impaired malignant cell outgrowth at metastatic sites. Single-cell RNA-sequencing of myCAF-depleted primary tumours revealed extensive transcriptional reprogramming across fibroblast, immune and malignant compartments, highlighting the complexity of assigning myCAF-to-malignant cell signalling mechanisms in vivo. To resolve this crosstalk, we co-cultured PDAC organoids with pancreatic stellate cells engineered to remain in myCAF or iCAF states. Cross-model transcriptomic analyses, together with genetic and pharmacological perturbation studies, showed that myCAF-derived TGF-{beta} directly promotes epithelial-to-mesenchymal transition signalling in PDAC malignant cells, providing a candidate mechanism for the reduced metastasis observed upon myCAF depletion in vivo. These findings reveal distinct, context-dependent roles for TGF-{beta}- and IL-1-dependent CAF states and identify myCAF-derived TGF-{beta} signalling as a stromal mechanism promoting malignant cell plasticity.

cancer biology↗